The musculoskeletal research field is becoming increasingly focused on studies at the genetic level. In particular, a variety of evaluation tools have recently been developed that allow investigators to understand the molecular systems in which biological processes occurs. The field of functional genomics seeks to annotate genomic sequence with assignments of gene and regulatory element identities and locations, RNA variants and abundance levels, and protein variants, abundances and interactions. As functional annotations accumulate, detailed and in-depth studies of specific genes and their products can be placed into a genomic context to reveal the molecular systems. In turn, those systems and processes can be studied using functional genomics techniques to identify the genes important for their regulation. One such technique is transcript profiling, the parallel quantitation of RNA abundance for thousands of genes. Transcript profiling can be open-ended, using methods that do not rely on previous knowledge of gene sequences, or closed to a defined set of probes for known RNAs. The Penn Microarray Facility provides instrumentation and expertise for RNA transcript profiling. The overall objective of this Microarray Core Facility is to develop and utilize genomic analyses directed toward problems of musculoskeletal tissue injury and repair. The Specific Aims are to: 1) provide guidance and training on the capabilities, advantages, and disadvantages, of various genomic protocols and analyses for musculoskeletal research through formal educational enrichment programs and through one-on-one interactions, 2) provide expertise and service for Affymetrix GeneChip assays, 3) provide expertise and service for the development and use of custom printed microarrays, 4) facilitate access to training and bioinformatics tools appropriate for analyzing the data produced in Aims 2 and 3, and 5) provide funding for development of new projects and collaborations and to develop preliminary and/or feasibility data for investigators. Successful completion of these aims will significantly enhance the environment and the capabilities of researchers at the University of Pennsylvania, leading to the development of novel and innovative approaches to musculoskeletal disorders.